[AMBER] Distance restraint for PMEMD

From: Abir Ganguly <ag1508.connect.rutgers.edu>
Date: Thu, 19 Jul 2018 08:48:20 -0400

Dear AMBER users,

I am trying to apply a harmonic restraint to a d1-d2 coordinate, where d1 and d2 are distances between the COMs of groups of atoms. I found an earlier thread on this topic and tried the following in the restraint file-

 iat=-1,-1,-1,-1, igr1=3595, 3596, igr2=3028,
 igr3=3028, igr4=3032,
 rstwt=1,-1,           r1=-999, r2=3.6, r3=3.6, r4=999, rk1=10, rk2=10,

In this case my coordinate is :  distance[COM(3595,3596) -- 3028] - distance[3028 -- 3032]

I tried with both pmemd and sander; with pmemd I am getting the error :

At line 1032 of file nmr_calls.F90 (unit = 33, file = 'rest.RST')
Fortran runtime error: Bad data for namelist object igr4
srun: error: cuda001: task 0: Exited with exit code 2
srun: Terminating job step 7013508.0

with sander I am getting the error :

forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 33, file /scratch/ag1508/work/vs/dimer/with_mg/c634/trunc3/wt/gdp_ap/str3/12_6_4/pmf/mg/temp2/rest.RST

I guess I am messing up the syntax of the restraint file. I will appreciate if anyone can point out any obvious errors with the input.

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Received on Thu Jul 19 2018 - 06:00:03 PDT
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